Variant report

Variant	rs4801861
Chromosome Location	chr19:39224413-39224414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39223740-39225954	U87	brain:	n/a	n/a
2	SIN3AK20	chr19:39223100-39226358	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39223292-39226313	MCF-7	breast:	n/a	n/a
4	PBX3	chr19:39223832-39226377	A549	lung:	n/a	n/a
5	JUND	chr19:39223167-39226365	A549	lung:	n/a	chr19:39224435-39224443 chr19:39224433-39224445 chr19:39224431-39224442
6	POLR2A	chr19:39223119-39224877	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:39224174-39224431	GM12878	blood:	n/a	n/a
8	FOS	chr19:39224230-39224643	HUVEC	blood vessel:	n/a	chr19:39224435-39224443 chr19:39224433-39224444 chr19:39224433-39224445 chr19:39224431-39224442
9	POLR2A	chr19:39224127-39224608	HUVEC	blood vessel:	n/a	n/a
10	SIN3AK20	chr19:39223820-39224881	A549	lung:	n/a	n/a
11	POLR2A	chr19:39223998-39224526	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:39221228-39226317	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:39223763-39225544	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:39224120-39224418	ProgFib	skin:	n/a	n/a
15	POLR2A	chr19:39223123-39224907	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:39223097-39225075	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr19:39224184-39224430	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:39224380-39225333	GM12891	blood:	n/a	n/a
19	POLR2A	chr19:39223643-39226161	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr19:39223236-39226266	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:39224035-39224635	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:39223887-39224749	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr19:39223136-39226382	A549	lung:	n/a	chr19:39225279-39225290 chr19:39225280-39225289 chr19:39224434-39224443
24	POLR2A	chr19:39223909-39226321	ECC-1	luminal epithelium:	n/a	n/a
25	SIX5	chr19:39223165-39226400	A549	lung:	n/a	chr19:39223670-39223684
26	POLR2A	chr19:39223118-39224864	HCT-116	colon:	n/a	n/a
27	POLR2A	chr19:39223694-39224689	HL-60	blood:	n/a	n/a
28	POLR2A	chr19:39224056-39224422	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:39221071-39225757	HepG2	liver:	n/a	n/a
30	YY1	chr19:39223085-39225646	A549	lung:	n/a	chr19:39223373-39223384
31	POLR2A	chr19:39223952-39224456	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:39223889-39225847	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr19:39223886-39224482	H1-hESC	embryonic stem cell:	n/a	n/a
34	FOSL2	chr19:39223785-39226303	A549	lung:	n/a	chr19:39224435-39224443 chr19:39224433-39224445 chr19:39224431-39224442
35	POLR2A	chr19:39223209-39224627	HCT-116	colon:	n/a	n/a
36	USF1	chr19:39224085-39225758	A549	lung:	n/a	n/a
37	POLR2A	chr19:39206681-39226302	PANC-1	pancreas:	n/a	n/a
38	REST	chr19:39223767-39224881	PANC-1	pancreas:	n/a	chr19:39224081-39224094
39	ZBTB33	chr19:39224013-39226329	A549	lung:	n/a	n/a
40	POLR2A	chr19:39221828-39226356	U87	brain:	n/a	n/a
41	ATF3	chr19:39224094-39225709	A549	lung:	n/a	n/a
42	POLR2A	chr19:39223737-39226322	A549	lung:	n/a	n/a
43	FOS	chr19:39224402-39224472	MCF10A-Er-Src	breast:	n/a	chr19:39224435-39224443 chr19:39224433-39224444 chr19:39224433-39224445 chr19:39224431-39224442
44	TCF12	chr19:39223818-39224426	A549	lung:	n/a	n/a
45	FOS	chr19:39224371-39224580	MCF10A-Er-Src	breast:	n/a	chr19:39224435-39224443 chr19:39224433-39224444 chr19:39224433-39224445 chr19:39224431-39224442
46	MTA3	chr19:39224092-39225326	GM12878	blood:	n/a	n/a
47	JUND	chr19:39224006-39224895	A549	lung:	n/a	chr19:39224435-39224443 chr19:39224433-39224445 chr19:39224431-39224442
48	POLR2A	chr19:39224206-39225183	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr19:39223143-39225790	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr19:39220891-39226327	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39224370-39224420	NB4	blood:	n/a
2	chr19:39224370-39224420	ProgFib	skin:	n/a
3	chr19:39224370-39224420	U87	brain:	n/a
4	chr19:39224370-39224420	Hela-S3	cervix:	n/a
5	chr19:39224370-39224420	SAEC	small airway:	n/a
6	chr19:39224370-39224420	PANC-1	pancreas:	n/a
7	chr19:39224370-39224420	HEK293	kidney:	embryo
8	chr19:39224370-39224420	PFSK-1	brain:	n/a
9	chr19:39224370-39224420	GM12892	blood:	n/a
10	chr19:39224370-39224420	HMEC	breast:	n/a
11	chr19:39224370-39224420	AG09319	gingival:	n/a
12	chr19:39224370-39224420	PrEC	prostate:	n/a
13	chr19:39224370-39224420	HRPEpiC	eye:	n/a
14	chr19:39224370-39224420	HRCEpiC	kidney:	n/a
15	chr19:39224370-39224420	HCT-116	colon:	n/a
16	chr19:39224370-39224420	A549	lung:	n/a
17	chr19:39224370-39224420	MCF10A-Er-Src	breast:	n/a
18	chr19:39224370-39224420	H1-hESC	embryonic stem cell:	embryo
19	chr19:39224370-39224420	HPAEpiC	pulmonary alveolar:	n/a
20	chr19:39224370-39224420	BE2_C	brain:	n/a
21	chr19:39224370-39224420	T-47D	breast:	n/a
22	chr19:39224370-39224420	HRE	kidney:	n/a
23	chr19:39224370-39224420	SK-N-MC	brain:	n/a
24	chr19:39224370-39224420	GM12891	blood:	n/a
25	chr19:39224370-39224420	RPTEC	kidney:	n/a
26	chr19:39224370-39224420	GM06990	blood:	n/a
27	chr19:39224370-39224420	HL-60	blood:	n/a
28	chr19:39224370-39224420	SK-N-SH_RA	brain:	n/a
29	chr19:39224370-39224420	NH-A	brain:	n/a
30	chr19:39224370-39224420	HUVEC	blood vessel:	n/a
31	chr19:39224370-39224420	IMR90	lung:	fetal
32	chr19:39224370-39224420	GM19239	blood:	n/a
33	chr19:39224370-39224420	HIPEpiC	eye:	n/a
34	chr19:39224370-39224420	AoSMC	blood vessel:	n/a
35	chr19:39224370-39224420	Jurkat	blood:	n/a
36	chr19:39224370-39224420	LNCaP	prostate:	n/a
37	chr19:39224370-39224420	AG04450	lung:	fetal
38	chr19:39224370-39224420	HAEpiC	amniotic membrane:	n/a
39	chr19:39224370-39224420	BJ	skin:	n/a
40	chr19:39224370-39224420	AG10803	skin:	n/a
41	chr19:39224370-39224420	K562	blood:	n/a
42	chr19:39224370-39224420	ECC-1	luminal epithelium:	n/a
43	chr19:39224370-39224420	MCF-7	breast:	n/a
44	chr19:39224370-39224420	HCM	heart:	n/a
45	chr19:39224370-39224420	NHBE	bronchial:	n/a
46	chr19:39224370-39224420	HCF	heart:	n/a
47	chr19:39224370-39224420	HCPEpiC	choroid plexus:	n/a
48	chr19:39224370-39224420	NHDF-neo	bronchial:	n/a
49	chr19:39224370-39224420	AG04449	skin:	fetal
50	chr19:39224370-39224420	ovcar-3	ovarian:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39224374..39227247-chr19:39227661..39229256,2	MCF-7	breast:
2	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
3	chr19:39217752..39221022-chr19:39222465..39225520,5	MCF-7	breast:
4	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
5	chr19:39138134..39140195-chr19:39224165..39225829,2	K562	blood:
6	chr19:39033166..39035444-chr19:39222579..39224639,2	K562	blood:
7	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
8	chr19:39223964..39228282-chr19:39327392..39332302,8	MCF-7	breast:
9	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:
10	chr19:39137588..39140195-chr19:39223883..39225829,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LGALS7-1	chr19:39223761-39226312	NONHSAT066236

No data

Variant related genes	Relation type
ENSG00000267892	TF binding region
ENSG00000267892	CpG island
ENSG00000267892	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1031849	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10421863	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs10424568	0.90[CHD][hapmap];0.87[JPT][hapmap]
rs1060186	0.89[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11665964	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12462503	0.92[CHD][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]
rs12984247	0.89[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap]
rs1564203	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2080988	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2112649	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3786841	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3786843	0.85[EUR][1000 genomes]
rs4347742	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802743	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508813	0.89[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap]
rs6508814	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7252630	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs749701	0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs752067	0.92[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap]
rs8099948	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8107877	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs888997	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs9304576	0.95[CHD][hapmap];0.87[JPT][hapmap]
rs9304577	0.82[JPT][hapmap]
rs936524	0.94[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4801861	RPS16	cis	parietal	SCAN
rs4801861	MEGF8	cis	cerebellum	SCAN
rs4801861	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs4801861	CAPN12	cis	Adipose Subcutaneous	GTEx
rs4801861	PPP1R13L	cis	cerebellum	SCAN
rs4801861	ERF	cis	cerebellum	SCAN
rs4801861	SFRS16	cis	parietal	SCAN
rs4801861	C19orf54	cis	parietal	SCAN
rs4801861	CAPN12	cis	Heart Left Ventricle	GTEx
rs4801861	CAPN12	cis	Esophagus Muscularis	GTEx
rs4801861	CAPN12	cis	multi-tissue	Pritchard
rs4801861	LGALS17A	cis	cerebellum	SCAN
rs4801861	CAPN12	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39214000-39224800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:39215600-39224800	Genic enhancers	A549	lung
4	chr19:39218000-39225000	Weak transcription	Primary T cells from cord blood	blood
5	chr19:39218000-39226800	Weak transcription	Psoas Muscle	Psoas
6	chr19:39218400-39224600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:39218600-39225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:39218800-39225200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:39218800-39226600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:39219400-39224600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr19:39220800-39224600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr19:39220800-39226800	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:39221200-39225400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:39221200-39226000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:39221800-39224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:39222000-39225200	Enhancers	Pancreas	Pancrea
17	chr19:39222200-39224800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:39222200-39225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:39222200-39226200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr19:39222200-39226800	Weak transcription	Brain Substantia Nigra	brain
21	chr19:39222400-39224800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:39222400-39224800	Weak transcription	Fetal Brain Female	brain
23	chr19:39222400-39225000	Enhancers	Duodenum Mucosa	Duodenum
24	chr19:39222400-39225400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:39222400-39226200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:39222400-39226600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:39222400-39226800	Weak transcription	Brain Angular Gyrus	brain
28	chr19:39222400-39226800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:39222600-39224800	Enhancers	Stomach Mucosa	stomach
30	chr19:39222600-39225000	Weak transcription	K562	blood
31	chr19:39222600-39225200	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr19:39222600-39225600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr19:39222600-39225800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:39222600-39226800	Weak transcription	Fetal Heart	heart
35	chr19:39222600-39227200	Weak transcription	Fetal Kidney	kidney
36	chr19:39222800-39224800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:39222800-39225200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:39222800-39225200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:39222800-39225200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:39222800-39225200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr19:39222800-39225200	Enhancers	Spleen	Spleen
42	chr19:39222800-39225400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:39222800-39226600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:39222800-39226600	Weak transcription	Brain Hippocampus Middle	brain
45	chr19:39222800-39226800	Weak transcription	Brain Anterior Caudate	brain
46	chr19:39222800-39226800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:39222800-39227400	Weak transcription	Aorta	Aorta
48	chr19:39223000-39224600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr19:39223000-39224600	Enhancers	Stomach Smooth Muscle	stomach
50	chr19:39223000-39225800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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